It's certainly something that's possible. In my experience, it's a consideration that comes up when departments ask Treasury Board and the Department of Finance for funding. I'm talking about the part that concerns administrative costs. That said, it's not a very important consideration.
Imposing a uniform limit would probably have adverse consequences, especially for programs where there is a need for auditing and enforcement. However, it would certainly be possible to impose a limit, allowing some flexibility for cases where more administrative or monitoring and compliance expenses are required.